rstan not using chain_id if `auto_write=TRUE`

Summary:

Saved models appear to also save the chain_id

Description:

https://groups.google.com/forum/#!category-topic/stan-users/UR5oaPsfjjE

Reproducible Steps:

library(rstan)

rstan_options(auto_write=FALSE)
stan(model_code="parameters { real x; } model { x ~ normal(0, 1); }", chain_id=5:8)  # uses chain_id 5:8

rstan_options(auto_write=TRUE)
options(mc.cores = parallel::detectCores())
stan(model_code="parameters { real x; } model { x ~ normal(0, 1); }", chain_id=5:8)  # uses chain_id 1:4

Current Output:

> stan(model_code="parameters { real x; } model { x ~ normal(0, 1); }", chain_id=5:8)  # uses chain_id 1:4
starting worker pid=41923 on localhost:11822 at 09:10:36.374
starting worker pid=41931 on localhost:11822 at 09:10:36.567
starting worker pid=41939 on localhost:11822 at 09:10:36.732
starting worker pid=41947 on localhost:11822 at 09:10:36.881

SAMPLING FOR MODEL 'd4901852a59d5abb2b87f654d5e8d0a7' NOW (CHAIN 1).

Expected Output:

> stan(model_code="parameters { real x; } model { x ~ normal(0, 1); }", chain_id=5:8)  # uses chain_id 1:4
starting worker pid=41923 on localhost:11822 at 09:10:36.374
starting worker pid=41931 on localhost:11822 at 09:10:36.567
starting worker pid=41939 on localhost:11822 at 09:10:36.732
starting worker pid=41947 on localhost:11822 at 09:10:36.881

SAMPLING FOR MODEL 'd4901852a59d5abb2b87f654d5e8d0a7' NOW (CHAIN 5).

RStan Version:

2.9.0-3

R Version:

3.2.4

Operating System:

OS X 10.11.4 (El Capitan)

Reproduce the issue through rstan_options(auto_write=TRUE) and the stan() entry point, comparing it with auto_write=FALSE. Trace how the chain_id argument is handled when a saved model is reused. Done means chain_id=5:8 produces sampling output beginning with CHAIN 5 under auto_write=TRUE, matching the expected behavior.